title: Mouse HSC - IC

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

description: Single cell RNA-seq data from mouse HSC after 48-hour in vitro treatment with DFO

data_processing:
Quality of sequencing reads was assessed with FastQC v0.11.9, overrepresented sequences and adapter contamination were filtered using TrimGalore v0.6.5.
Cell barcode processing, transcriptome alignment (mm10), and gene UMI counting were performed for each of the samples using the count module of Cell Ranger v3.0.2.
Cells with UMI counts <2,000 or >10,000 were excluded from further analysis to rule out contamination from potentially dead or non-single cells. Cells with mitochondrial mRNA >15% were also excluded. Moreover, genes that were expressed in less than 50 cells were excluded from the expression matrix for downstream analysis.
The expression data was then normalized by the total number of unique reads, multiplied by a scale factor of 10,000 and log-transformed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized levels for every gene and every sample

source_name: Mouse HSC after 48-hour in vitro treatment with DFO

growth_protocol: Mouse HSC (Lineage−c-Kit+Sca-1+CD150+CD48−) were sorted, and cultured in Myelocult M5300 medium (Stem Cell Technologies) supplemented with 100 ng/ml rmSCF (Gemini Bio-Products, CA), 50 ng/ml rmTPO (Gemini Bio-Products, CA) and 200 µg/ml Primocin (InvivoGen, San Diego, CA).

extract_protocol:
After treatment, cells were harvested and directly subjected to library preparation with 10x Genomics platform.
After treatment, 20,000 live cells from each experimental condition were subjected to 10x Genomics platform for library preparation using Chromium Single Cell 3′ Reagent Kits (v3) following the manufacturer’s sample preparation guide (PN CG00054 Rev B; Fluidigm).
Libraries were prepared with 10x Genomics platform, and 50ng libraries were sequenced on BGISEQ-500 platform with 28+8+91bp reads (read 1: 28bp; read 2: 91bp plus 8bp for index), at two lanes per sample.

treatment_protocol: Mouse HSC were treated with either DFO (10 μM, Sigma), or vehicle control (sterile water) in liquid culture for 48 hours.

value: FACS-sorted HSC

value: 6-8 weeks


title: Control_1

status: Public on May 02 2024

type: SRA

city: Tianjin

first: Ting

last: Zhou

address: Qixiangtai road 22

country: China

institute: Tianjin medical university

library_source: transcriptomic

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: HUVECs

growth_protocol: HUVECs were cultured in M199 supplemented with 10%FBS and antibodies in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
HUVECs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using  oligo -dT beads

treatment_protocol: The cells were treated with 1 μM 17,18-EEQ for 24 hours until growth of 70% confluence

tag: cell line

value: HUVECs

tag: cell type

value: Endothelial cells

tag: genotype

value: Wild type

tag: treatment

value: PBS


title: AD_+ND1, replicate1, scRNA-seq

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

institute: Jinan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were processed with fastQC and fastp to remove low quality reads. Poly-A tails and adaptor sequences were removed by Cutadapt. After quality control, reads were mapped to the reference genome using STAR. Gene counts and UMI counts were acquired by FeatureCounts software. Expression matrix files for subsequent analyses were generated based on gene counts and UMI counts.
Assembly: mm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Fresh hippocampus was removed with tweezers and then dissociated into single cell suspension using the papain kit (Worthington) according to manufacturer’s protocol. The cell suspension was injected into the SCOPE-chip™ microfluidic chip to complete the separation of single cells based on the principle of "Poisson distribution". Cells fell into specially customized chip microwells under the influence of gravity, ensuring that only one cell fell into each microwell.
The magnetic beads in the chip were collected, and the mRNA captured by the magnetic beads was reverse transcribed into cDNA and amplified. After cDNA fragmentation, adapter ligation and other necessary steps, a sequencing library suitable for the Illumina sequencing platform was constructed.

tag: tissue

value: Hippocampus

tag: time

value: 6 months

value: Brain cells

tag: strain


title: Ctrl_+GFP, replicate1, scRNA-seq

description: 10x Genomics


title: ND liver tissue, bio rep 1

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Adaptor sequences were removed from raw data using Trimmomatic (ver. 0.39.0).
Sequencing reads after trimming were aligned to a mouse reference genome sequence (GRCm38/mm10) in the HISAT2 (ver. 2.2.1).
Read counts per gene were calculated using featureCounts (ver.2.0.1) based on GENCODE gene annotation version M25.
The transcripts per million (TPM) normalization was done according to the length of each gene and the sum of mapped reads.
Assembly: GRCm38/mm10

source_name: Liver

extract_protocol:
Total RNA from sorted cells was extracted with TRIzol LS reagent, Favorgen RNA Kit (Favorgen)
RNA-seq libraries were prepared using the  Nextera XT Kit (Illumina).

value: Liver

value: WT

value: Normal diet


title: CDA-HFD7w liver tissue, bio rep 1

value: CDA-HFD 7w


title: CDA-HFD7w liver tissue, bio rep 3


title: Lyz2cre/+.Egr2fl/fl, bio rep 3

data_processing:
Adaptor sequences were removed from raw data using Trimmomatic (ver. 0.39.0).
Sequencing reads after trimming were aligned to a mouse reference genome sequence (GRCm38/mm10) in the HISAT2 (ver. 2.2.1).
Read counts per gene were calculated using featureCounts (ver.2.0.1) based on GENCODE gene annotation version M25.
The transcripts per million (TPM) normalization was done according to the length of each gene and the sum of mapped reads.
Assembly: GRCm38/mm10
Supplementary files format and content: fastq

source_name: Liver macrophages

extract_protocol:
Total RNA from sorted cells was extracted with an RNeasy Micro Kit (QIAGEN).
RNA-seq libraries were prepared using the NEBNext UltraII Directional RNA Library Prep Kit (NEW ENGLAND BioLabs).

value: Liver macrophages

value: CDA-HFD


title: ND liver tissue, bio rep 2


title: D27_3 GEX

city: Melbourne

first: Hyun Jae

last: Lee

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

description:
10x Genomics
d27_3_barcodes.tsv.gz
d27_3_features.tsv.gz
d27_3_matrix.mtx.gz

data_processing:
Data was processed using the “cellranger multi” pipeline from Cell Ranger version 6.1.1 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Polyclonal CD4+ T cells from spleens were isolated by flow cytometry into a 2% BSA/PBS buffer. For each timepoint, samples from each individual mouse replicate were labelled with a different hashtag reagent, and samples from 5 individual mouse replicates were pooled for isolating different populations of CD4+ T cells. At Day 30 and Day 3 after re-infection, CXCR3-/CD11a-low (marking naive cells) and CXCR3+/CD11a-high CD4+ T cells were sorted and pooled at a proportion of 1:9. Polyclonal CD4+ cells were sorted as single-cells using the Chromium 10x Genomics platform. Approximately 33,000 cells were loaded per channel onto a Chromium controller (10x Genomics) for generation of gel bead-in-emulsions using 10x Genomics Single Cell 5' Reagent Kit v2 (single-cell gene expression and immune repertoire profiling).
Sequencing libraries were prepared using Single Cell 5’ Reagent Kits v2 (10x Genomics) and then converted using the MGIEasy Universal Library Conversion Kit (BGI).

value: Spleen

value: CD4-positive alpha-beta T cell

tag: age

value: 6-12 weeks


title: Lyz2cre/+.Egr2fl/fl, bio rep 2


title: Lyz2cre/+.Egr2fl/fl, bio rep 1


title: Egr2fl/fl, bio rep 3


title: Egr2fl/fl, bio rep 2


title: Egr2fl/fl, bio rep 1


title: Mouse HSC - Control

country: USA

description: Single cell RNA-seq data from mouse HSC after 48-hour in vitro treatment with vehicle control

source_name: Mouse HSC after 48-hour in vitro treatment with vehicle control

value: FACS-sorted HSC

value: 6-8 weeks


title: WT, rep2

city: Aurora

first: Tonya

last: Brunetti

state: CO

address: 12800 East 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina universal adapters were removed, bases were trimmed if the Phred Score was less than 20, and any reads after trimming that were fewer than 10 base pairs in length were discarded using Cutadapt v4.4 under Python version 3.10.
Reads were aligned and quantified to the mm10 reference genome using STAR v2.7.10b
any genes with less than 10 counts total summed across all 6 samples were removed from the analysis
Counts were normalized using DESeq2 v1.36.0 and 2 RUVs were added as covariates to the generalized linear model using RUVSeq v1.30.0
Assembly: mm10
Supplementary files format and content: MCJ_KO_vs_WT_results_deseq2_regress_surrogate_RUV_K2_vars.csv contains comma-separated differential expression results for all genes considered in DE analysis
Supplementary files format and content: counts_matrix.rds is an R data file that contains the raw counts for all genes for each sample; can be read into R using readRDS()

source_name: mouse spleen lymphnodes

growth_protocol: Bruff/s medium + 5% FBS + IL2

extract_protocol:
Total RNA is isolated using RNeasy Micro Kit (Qiagen, Catt# 74004). The genomic DNA were removed using DNase I treatment as recommended by the manufacturer (Qiagen).
The Tecan Universal Plus mRNA-Seq Library Kit was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries.

value: mouse spleen lymphnodes

value: primary mouse T cells

value: CD8+ CAR T cells


title: MCJ KO, rep3


title: WT, rep1


title: WT, rep3


title: MCJ KO, rep1


title: Pmel-1 CD8 T cells primed in WT mice as control, scRNAseq

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

institute: Henry Ford Health

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger-6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
For isolation of adoptively transferred Pmel-1 Thy1.1+ CD8+ T cells, spleen cells from immunized mice were first enriched with anti-Thy1.1 magnetic microbeads and sorted using BD FACSAira II
scRNA-seq libraries were generated using the 10X Genomics Chromium Single Cell 3′ Reagent Kit (v2 Chemistry) and Chromium Single Cell Controller as described in the manufacturer's  instructions. Briefly, FACS-sorted cells were loaded into each reaction for gel bead-in-emulsion (GEM) generation and cell barcoding. Reverse transcription of the GEM (GEM-RT) was performed using a Veriti™ 96-Well Fast Thermal Cycler (Applied Biosystems) at 53 °C for 45 min, 85 °C for 5 min, and a 4 °C hold. cDNA amplification was performed after GEM-RT cleanup with Dynabeads MyOne Silane (Thermo Fisher Scientific) using the same thermocycler (98 °C for 3 min, 98 °C for 15 s, 67 °C for 20 s, 72 °C for 1 min, followed by a 12 cycle repeat at 72 °C for 1 min and a 4 °C hold). Amplified cDNA was cleaned up with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA) that was followed by a library construction procedure, including fragmentation, end repair, adapter ligation, and library amplification. An Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) was used for library quality control. Libraries were sequenced on an Illumina HiSeq4000 using a paired-end flow cell: Read 1, 26 cycles; i7 index, 8 cycles; Read 2, 98 cycles.

value: spleen

value: CD8 T

value: immunization with anti-DEC-205-hgp100 plus adjuvant CpG


title: Pmel-1 CD8 T cells primed in CD11c-b-catenin active mice, scRNAseq

description: 10X Genomics

value: CD11c-b-catenin active


title: iMEPM, plusPDGF_AA, shSrsf3, rep3

first: Katherine

middle: Ann

last: Fantauzzo

address: 12801 East 17th Avenue, MS 8120

department: Craniofacial Biology

data_processing:
For differential expression analysis, read trimming and filtering with Bbduk (v35.85), transcript abundance with Salmon (v1.4.0), gene-level summarization with tximport, differential expression testing using DESeq2 (v1.32.0)
For alternative splicing analysis, read alignment with STAR (v.2.7.9a), alternative splicing detection with rMATS (v.4.0.2)
Assembly: GRCm39 (Genocde M26)
Supplementary files format and content: Gzip Archive of Salmon output per sample
Supplementary files format and content: TSV file of Salmon estimated raw counts
Supplementary files format and content: Excel spreadsheet of DESeq2 output
Supplementary files format and content: Excel spreadsheets of pairwise rMATS analysis output

source_name: iMEPM

growth_protocol: DMEM, 10% fetal bovine serum, 50 U/mL penicillin, 50 ug/mL streptomycin, 2 mM L-glutamine.  37 degrees C in 5% CO2. Stable cell lines were created by growing cells in the presence of medium containing lentivirus with scramble shRNA (vectorID: VB010000-0009mxc) or Srsf3 shRNA (vectorID: VB900060-7699yyh) and 10 ug/mL polybrene for 16 hours, follwed by 10 days of 4 ug/mL puromycin selection.  GFP expressing cells were sorted and expanded for 9-20 passages for experimentation.

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen)
Total RNA (200 ng) used for Universal Plus mRNA-seq kit (Tecan group)

treatment_protocol: Scramble and Srsf3 shRNA cells were left unstimulated or treated with PDGF-AA ligand (10 ng/mL) for 1 hour

value: iMEPM

value: mouse embryonic palatal mesenchyme

value: PDGF-AA

tag: shRNA


title: iMEPM, plusPDGF_AA, shSrsf3, rep1


title: ND liver tissue, bio rep 3

value: Liver

value: WT

value: Normal diet


title: CDA-HFD7w liver tissue, bio rep 2

value: CDA-HFD 7w


title: MCJ KO, rep2


title: iMEPM, plusPDGF_AA, shScramble, rep1

value: Scramble


title: iMEPM, plusPDGF_AA, shSrsf3, rep2


title: iMEPM, plusPDGF_AA, shScramble, rep2


title: iMEPM, minusPDGF_AA, shSrsf3, rep2

value: untreated


title: iMEPM, minusPDGF_AA, shSrsf3, rep3


title: iMEPM, plusPDGF_AA, shScramble, rep3


title: iMEPM, minusPDGF_AA, Srsf3 IP, rep2

data_processing:
Adapter trimming by cutadapt (v.1.18), quality filtering and barcode collapsing using FASTQ-Toolkit (v.0.0.14), seqtk (v.1.3-r106) and custom scripts.
Reads were mapped against a repetitive element index created from sequences of msRepDB. Reads not mapping to repetitive elements were mapped to the mouse genome (GRCM38 Gencode M26) using STAR (2.7.9.a; alignEndsType: EndtoEnd and outFilterMismatchNoverReadLmax: 0.04).
Peak calling was performed using omniCLIP (v.0.20; --fg_pen 5). Peak annotation and motif analysis were performed using RCAS (v1.19.0) and custom R script.
Assembly: GRCm39 (Genocde M26)
Supplementary files format and content: Excel spreadsheet with peak call locations at the gene-level

growth_protocol: DMEM, 10% fetal bovine serum, 50 U/mL penicillin, 50 ug/mL streptomycin, 2 mM L-glutamine.  37 degrees C in 5% CO2.

extract_protocol:
eCLIP was performed according to Van Nostrand et al 2016, 2017. 2 million cells were UV-crosslinked, lysed and subject to IP with IgG or an Srsf3 antibody. IP samples underwent dephosphorylation, on-bead RNA adapater ligation, isolation and proteinase K digestion. RNA was isolated with acid phenol/chloroform/isoamyl alcohol (pH 6.5) and reverse transcribed with Superscript III (Thermo Fisher Scientific).  ExoSAP-IT (Affymetrix) was used to remove excess primers.
DNA adapters were 3’ ligated, and samples were cleaned up with Dynabeads MyOne Silane (Thermo Fisher).  Libraries were PCR amplified using Q5 PCR mix (New England Biolabs) for 16-25 cycles and sequenced on an Illumina NOVASEQ 6000

treatment_protocol: Cell were left unstimulated or treated with PDGF-AA ligand (10 ng/mL) for 1 hour

tag: eclip antibody


title: iMEPM, minusPDGF_AA, shScramble, rep3


title: iMEPM, plusPDGF_AA, Srsf3 IP, rep2


title: iMEPM, minusPDGF_AA, shSrsf3, rep1


title: iMEPM, minusPDGF_AA, Srsf3 IP, rep1


title: iMEPM, minusPDGF_AA, shScramble, rep1


title: iMEPM, plusPDGF_AA, IgG IP

value: IgG


title: iMEPM, plusPDGF_AA, input

value: input


title: r3_2D_iWAT_PGM_woISO [D128]

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality control of reads sequences were assesed by FastQC (v0.11.9), FastQ_Screen (v0.15.1) and AdapterRemoval (v2.3.2).
Raw sequencing reads (fastq.gz files) were aligned to the mouse genome (mm39) employing STAR (v2.7.9a).
Various mapping quality control steps were undertaken, including the generation of statistics, index statistics, and flag statistics using Samtools (Samtools v1.15.1). Additional quality metrics were obtained through CollectAlignmentSummaryMetrics, QualityScoreDistribution, MeanQualityByCycle, CollectInsertSizeMetrics, CollectRnaSeqMetrics, using Picard (v2.25.5) and by and bamqc using Qualimap (v2.2.1).  Library complexity was evaluated using Preseq (v3.2.0) and PBC bottlenecking metrics which were computed using Bedtools (v2.30.0). Duplicates were identified but retained in the dataset using Picard MarkDuplicates. Filtering steps were applied to exclude reads with low mapping quality (MAPQ<30), reads/mates that were unmapped, reads failing platform and those not classified as primary alignments (samtools view -q 30 -F 780).  For additional RNA-seq quality control, tools such as qualimap rnaseq (v2.2.1), rnaseqc (RNA-SeQC v2.4.2), and various metrics from RSeQC v4.0.0 (read_duplication, read_GC, inner_distance, junction_annotation, junction_saturation, bam_stat, infer_experiment, read_distribution, geneBody_coverage, and tin) were employed.  To summarize the diverse quality metrics, an HTML report was generated using MultiQC (v.1.14).
The quantification of read pairs in exonic regions was performed using featureCounts (Subread v2.0.3) with GENCODE vM33 GTF reference annotation and optional arguments -p --countReadPairs -t exon
Assembly: mm39
Supplementary files format and content: FeatureCounts output tab-delimited text file for each sample
Supplementary files format and content: tab-delimited text file containing the raw counts from each Sample

source_name: inguinal white adipose tissue

growth_protocol: The stromal vascular fraction from the inguinal white adipose tissue was cultured in either Preadipocyte Growth Medium (BulletKit, Lonza, PT-8002) or a combination of Preadipocyte Growth Medium and Endothelial Growth Medium (BulletKit, Lonza, CC-3162)

extract_protocol:
RNA was harvested using the chloroform extraction method in combination with purification using EconoSpin columns. 200 ng total RNA was used for construction of sequencing libraries
RNA libraries for RNA seq. was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina, NEB #E7775, following the manufacturer's instructions

treatment_protocol: To induce thermogenesis, 2D and 3D cultures were stimulated with the beta-adrenergic agonist Isoproterenol (Sigma, I5627) for 6 hours (final conc. 1 µM)

value: inguinal white adipose tissue

value: Stromal vascular fraction

value: Adipogenic differentiation


title: Diabetic + Vehicle (DV) 4

first: Assam

last: El-Osta

address: 75 Commercial Road

institute: Baker Heart and Diabetes Institute

description:
scRNA Drop-Seq
SCNOV_cell_idents.tsv
SCNOV_dge_allclusters.csv

data_processing:
Raw single-cell reads were processed using Drop-Seq tools version 2.4 including demultiplexing and retention of reads according to the top 3000 cell barcodes detected per sample, alignment of reads to mouse transcripts (GRCm38, Ensembl) and generation of transcript by cell count matrices
Count matrices were imported into R as Seurat objects using the R package Seurat version 3.0.1 . Subsequent quality filtering included removal of cells meeting any of the following criteria; cells having fewer than 400 or more than 3000 genes detected, cells with more than 20% of captured transcripts being mitochondrial. Quality filtered samples were normalised and integrated using Seurat functions NormalizeData and IntegrateData (dims=1:30) prior to clustering, which used PCA reduced dimensions (dims=1:23) for functions RunTSNE, FindNeighbors   and FindClusters (res=0.8) to assign clusters. To identify cell types, cluster specific gene signatures were examined with Seurat’s FindAllMarkers function and comparison with known endogenous marker gene expression
Differential gene expression was calculated using the Seurat function FindMarkers for each cluster identity specifying Wilcoxon rank sum analysis with min.pct set to 0.25
Assembly: GRCm38, Ensembl
Supplementary files format and content: SCNOV.*.mx.gz - Sample count matrix files contain demultiplexed feature~cell read counts formatted as tab separated values.
Supplementary files format and content: SCNOV_cell_idents.tsv - Cell Annotation file reporting cell-barcode with cell-Identity formatted as tab separated values
Supplementary files format and content: SCNOV_dge_allclusters.csv - Differential gene expression between groups for all cluster idents as generated and collated using the function FindMarkers (Seurat).

source_name: kidney

extract_protocol:
Preparation of kidney tissues was conducted at 4˚C with all buffers maintained on ice. Processed individually, each mouse kidney was collected and chilled in PBS before dissection of kidney cortex. The isolated cortex material was initially minced using a scalpel and pressed through a 100µM cell sieve using a 1 mL syringe plunger while rinsing material through with PBS. The resulting homogenate was collected in a 50 mL falcon tube and centrifuged at 250 x G for 2 minutes and the supernatant discarded. The pellet was resuspended in 20 mL PBS and poured through a 70 µM sieve to capture glomeruli while allowing smaller structures to pass through. The “glomerular fraction" caught by the sieve was transferred to a 15 mL falcon tube using a Pasteur pipette with a volume of PBS up to 15 mL. The recovered fraction was centrifuged at 200 x G for 5 minutes, after which the supernatant was carefully removed to avoid disturbing pelleted material. The glomerular pellet was resuspended in 1 mL of digestion buffer (10 mg protease from bacillus licheniformis, 10uL DNase, 1uL 0.5 M EDTA, 1mL PBS), and allowed to digest for 13 minutes at 4˚ C with slow rotation. Further digestion was stopped by the addition of 1 mL of 20 % FBS in PBS. To aid dissociation, the mixture was additionally triturated using a 1000 µL pipette very gently. Triturated material was passed through a 40 µM cell sieve and collected in a 50 mL falcon tube by rinsing through with 2% FBS in PBS. Material that did not pass through the 40 µM sieve was further triturated until no remaining clumps remained on the sieve. Immediately prior to starting single cell capture, the dissociated glomerular fraction was centrifuged at 200 x G for 5 minutes, followed by repeated washes (at least 3 washes of 200 x G, 1 mL filtered PBS with 0.01% BSA, 2 minutes) to reduce free RNA in solution
Single-cell capture and transcriptome profiling were conducted using a droplet based technology “Drop-Seq” and a single-cell microfluidics platform designed by Dolomite-Bio according to “Drop-Seq Protocol version 3.1 Dec-2015” with minor modifications. Modifications include the use of Terra PCR Direct Polymerase Mix for cDNA  amplification steps with 4 cycles in stage one and 11 cycles in stage two). Final sample libraries were created using the Nextera XT DNA Library Preparation Kit and sequenced using Illumina HiSeq in paired-end 150-cycle configuration by NovogeneAIT Genomics (Singapore).

treatment_protocol: Diabetic Ins2Akita mice (C57BL/6-Ins2Akita/J) and their WT counterparts were purchased from the Jackson Laboratory (Strain #003548, Bar Harbor, ME, USA) and 6 weeks of age, male WT or heterozygous Ins2Akita mice were randomly assigned to receive either vehicle (PBS-Tween 80), or liraglutide (Lira, 50μg/kg) by daily subcutaneous injection for 20 weeks

value: mixed

value: kidney

value: C57BL/6 - Ins2Akita/J

value: Ins2 / Ins2Akita

value: Vehicle

tag: disease state

value: Diabetic

value: 26 weeks


title: r2_2D_iWAT_PGM_wISO [D121]

value: WT

value: Adipogenic differentiation, Isoproteronol treatment

value: Isoproterenol (Sigma, I5627) for 6 hours (final conc. 1 µM)


title: r2_3D_iWAT_EGM-PGM_wISO [D120]

value: Angiogenic and adipogenic differentiation, Isoproteronol treatment


title: r3_2D_iWAT_PGM_wISO [D127]


title: r2_2D_iWAT_PGM_woISO [D122]


title: Diabetic + Vehicle (DV) 3


title: Diabetic + Vehicle (DV) 2


title: r1_2D_iWAT_PGM_woISO [D116]


title: Diabetic + Vehicle (DV) 1


title: Diabetic + Liraglutide (DL) 4

value: Liraglutide 50ug/kg/day


title: iMEPM, minusPDGF_AA, IgG IP

value: iMEPM

value: mouse embryonic palatal mesenchyme

value: untreated

value: IgG


title: r1_3D_iWAT_EGM-PGM_wISO [D114]

value: inguinal white adipose tissue

value: Stromal vascular fraction


title: Diabetic + Liraglutide (DL) 2

value: mixed

value: kidney


title: iMEPM, minusPDGF_AA, shScramble, rep2

value: Scramble


title: Diabetic + Liraglutide (DL) 3

value: C57BL/6 - Ins2Akita/J

value: Ins2 / Ins2Akita


title: Control + Vehicle (CV) 5

value: Ins2 / Ins2

value: Vehicle

value: Control

value: 26 weeks


title: Diabetic + Liraglutide (DL) 1

value: Diabetic


title: Control + Vehicle (CV) 4


title: iMEPM, minusPDGF_AA, input

value: input


title: EpiKO_ZT20_4

city: Barcelona

first: Thomas

last: Mortimer

address: Carrer Baldiri Reixac 10-12

country: Spain

institute: IRB Barcelona

data_processing:
Quality control and adapter trimming was performed using Trimmomatic (version 0.36).
Reads were aligned to the mm10 genome (UCSC) using the HISAT2 aligner (version 2.2.1), and subsequently sorted using SAMtools (version 1.3.1). After alignment, read quantification was performed using featureCounts (version 1.6.0) and the resulting count data was then normalized to generate RPKM values using the edgeR ‘rpkm’ function (version 3.18.1).
To identify specific genes reliant upon different clock communication pathways for their rhythmic expression, the DryR algorithm was applied to compare this dataset with rhythmic in WT epidermis. Raw RNAseq counts were used as input, and the function ‘dryseq()’ was applied to run the algorithm. The resulting output was then filtered (BICW ≥ 0.9, Amp ≥ 0.25, Periodicity = 24 hours), to generate the gene sets then further analyzed.
Assembly: mm10
Supplementary files format and content: Text file (.txt) output from the DryR algorithm when applied to the diurnal RNA-seq data sets presented here and that of WT epidermis (as presented in GSE190032) . The file contains the probability that each gene is associated with a specific rhythmic gene model, along with other details on the rhythmicity parametres of the gene.

source_name: Skin

growth_protocol: Mice were kept in rooms at 22°C degrees with ad libitum access to a standard chow diet, under a 12h:12h light/dark cycle.

extract_protocol:
Mice were sacrificed at the relevant time by C02 asphyxiation, and their backskin was subsequently removed and stored in ice-cold PBS. The hypodermis was then removed from the skin by vigorous scraping using a scalpel. In a petri dish, the skin was floated on 10ml of 1mg/ml dispase (Sigma Aldrich) (in PBS) for 45 minutes at 37°C to enzymatically separate the epidermis. Using a scalpel, the epidermis was separated from the surface of the skin, and then mechanically disaggregated using surgical scissors. The disaggregated epidermis was placed into 10ml of ice cold PBS + 10% chelated FBS to inactivate dispase, and then sequentially filtered through 100µM and 40µM filters, giving a purified extract of epidermal cells. To extract total RNA, one million epidermal cells were lysed in 500µL TRIzol (Invitrogen), vortexed with 100µL chloroform, and then the resulting aqueous layer containing RNA was isolated. The aqueous layer was mixed with 825µL RLT buffer (Qiagen) and 625µL 100% ethanol to induce RNA precipitation. The sample was further processed using an RNeasy mini kit (Qiagen) in accordance with the manufacturers protocol, and RNA was eluted in molecular biology grade water.
Prior to library preparation, RNA integrity was estimated using an RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent). Libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) following the manufacturer´s recommendations. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 1x51bp+17bp+8bp using, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).

treatment_protocol: To profile daily transcriptional rhythms, for each genotype, the skin of four eight-week-old mice (all males) was collected at six time points throughout the day. Each time point was separated by four hours, with the first sample collected at lights on (ZT0/8:00am).

value: Skin

value: epidermal cell

tag: time point

tag: Sex

value: Male


title: EpiKO_ZT20_2


title: r3_3D_iWAT_EGM-PGM_wISO [D126]

value: WT

value: Angiogenic and adipogenic differentiation, Isoproteronol treatment

value: Isoproterenol (Sigma, I5627) for 6 hours (final conc. 1 µM)


title: r3_3D_iWAT_EGM-PGM_woISO [D124]

value: inguinal white adipose tissue

value: Stromal vascular fraction

value: Angiogenic and adipogenic differentiation


title: EpiKO_ZT20_3


title: Control + Vehicle (CV) 3

value: mixed

value: kidney

value: C57BL/6 - Ins2Akita/J


title: r1_3D_iWAT_EGM-PGM_woISO [D112]


title: EpiKO_ZT20_1


title: Control + Vehicle (CV) 2

value: Ins2 / Ins2

value: Vehicle


title: EpiKO_ZT16_4


title: Control + Liraglutide (CL) 4

value: Liraglutide 50ug/kg/day

value: Control

value: 26 weeks


title: Control + Vehicle (CV) 1


title: EpiKO_ZT16_3

value: Skin


title: EpiKO_ZT16_2

value: epidermal cell


title: EpiKO_ZT12_4

value: Male


title: Control + Liraglutide (CL) 2


title: EpiKO_ZT12_3


title: Control + Liraglutide (CL) 3


title: EpiKO_ZT12_2


title: Control + Liraglutide (CL) 1


title: FOG2input

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

description: FOG2 ChIP-seq on E12.5 heart ventricles

library_source: genomic

data_processing:
Single end reads were aligned to mouse genome version mm10 with bowtie2 version 2.3.2
Aligned reads were sorted with samtools version 1.5 before removing duplicates with Picard tool MarkDuplicates version 2.8.1.
Reads with q < 30 were removed with samtools version 1.5
peaks were called with MACS2 version 2.1.1 combing all replicates to make one output
Fold enrichment bigwig  were generated with MACS2, then converted to bigWig files with UCSC tool bedgraphTobigWig
Assembly: mm10
Supplementary files format and content: narrowPeak file
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: embryonic heart ventricle

extract_protocol:
For each biological replicate, about 20 E12.5 Fog2flbio/flbio;Rosa26BirA/BirA (037509-JAX) heart ventricles were harvested and crosslinked in 1% formaldehyde in PBS for 10 minutes at room temperature. Chromatin was fragmented to 300-800 bp using a microtip sonicator (Qsonica, S-3000). Biotinylated FOG2 and bound chromatin was pulled down by incubation with streptavidin beads (ThermoFisher Scientific, Cat#11206D
Libraries were constructed using the KAPA HyperPrep ChIP-seq library preparation kit (Roche, cat# 07962347001)

tag: antibody

value: heart ventricle

value: WT


title: EpiKO_ZT8_3


title: EpiKO_ZT8_4


title: EpiKO_ZT4_4


title: output6.2

city: Basel

first: Guillaume

last: Diss

address: 66 Maulbeerstrasse

country: Switzerland

institute: FMI

library_source: other

data_processing:
For the barcode-variation association, reads were pre-processed with cutapdapt 1.18 and PEAR0.9.11, additional details in the corresponding manuscript
For the DMS, barcode reads were matched to the expected barcode sequences, aggregated by amino acid substitutions and processed with DimSum
Supplementary files format and content: tab-delimited text file. Contains count and logFC
Library strategy: Amplicon-Seq

molecule: other

organism: Saccharomyces cerevisiae

extract_protocol:
For the barcode variant association, DNA was extracted from the transformed E. coli cells using the NucleoBond® PC 500 kit (Macherey-Nagel, Düren, Germany). For the JUN DMS libraries, DNA was extracted using a custom yeast Midiprep protocol
Sequencing libraries were constructed by PCR with primers cotaining the illumina adapters


title: output4.2


title: output3.2


title: EpiKO_ZT8_2


title: FOG2rep2

description: FOG2 ChIP-seq on E12.5 heart ventricles


title: EpiKO_ZT12_1


title: FOG2rep1

description: FOG2 ChIP-seq on E12.5 heart ventricles


title: EpiKO_ZT4_3


title: output5.2


title: EpiKO_ZT8_1


title: output1.2


title: output5


title: EpiKO_ZT4_2


title: output4


title: EpiKO_ZT0_3


title: EpiKO_ZT0_4


title: EpiKO_ZT16_1


title: output3


title: EpiKO_ZT4_1


title: EpiKO_ZT0_2


title: output6


title: EpiKO_ZT0_1


title: output2.2


title: input5


title: input4


title: AT2 cells (CT26 Niche) rep2

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
fastq files were processed with the nf-core/atacseq pipeline v1.2.1with the flags "--min_reps_consensus 2 --macs_fdr 0.01"
normalised coverage track generation was done with BEDtools
peak calling was carried out with MACS2
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak

source_name: Alveolar type II cells

extract_protocol: The Omni ATAC-seq protocol was applied with few modifications. Omni ATAC-seq was performed on 50,000 FACS-purified AT2 cells from distal lung or metastatic niche of 4T1 and CT26 lung metastases. Briefly, purified AT2 cells were incubated in 50 μL of cold ATAC-seq resuspension buffer (RSB) for 3 min on ice and then diluted on RSB containing 0.1% Tween-20. Isolated nuclei were resuspended on transposition mix containing the Tn5 transposase (manufactured and assembled in house at a final concentration of 100 nM/reaction) for 30 min on 37 ºC. Transposed fragments were purified and cleaned using the AMPureXP beads (Beckman Coulter, A63881) as per the manufacturer’s instructions. The libraries were then pre-amplified, the required number of additional amplification cycles was manually assessed  and amplified again using the NEBNext High-Fidelity 2X PCR Master Mix (Thermo Fisher Scientific, M0541S). Finally, the libraries were purified once again using the AMPureXP beads and submitted for sequencing on NovaSeq 6000 (30 million reads/sample).

treatment_protocol: Cells (50,000) were FACS-sorted and immediately subjeted to Omni ATAC protocol.

value: Alveolar type II cells


title: input6


title: AT2 cells (CT26 Niche) rep1


title: AT2 cells (CT26 Distal) rep1


title: AT2 cells (4T1 Niche) rep3


title: AT2 cells (CT26 Distal) rep2


title: input3


title: input2


title: AT2 cells (4T1 Distal) rep3


title: input1


title: output2


title: AT2 cells (4T1 Niche) rep1


title: iPSC EC, wild-type, AMM2 treated

city: Stony Brook

first: Huichun

last: Zhan

state: NY

address: 101 Nicolls Rd

institute: Stony Brook Univeristy

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Differential expression analysis between two groups was performed using the edgeR R package (3.22.5). The resulting P-values were adjusted using the Benjamini and Hochberg’s method for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 found by edgeR were assigned as differentially expressed. Gene set enrichment analysis (GSEA) was performed using the complete list of genes according to their differential expression. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the ClusterProfiler R package. GO terms with corrected P-value less than 0.05 were considered significantly enriched.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene ID, readcount, FPKM, log2 fold change, p value, padj value, and gene information for each sample

growth_protocol: A pair of human induced pluripotent stem (iPS) cell lines (JAK2 wild-type PVB1.11 and JAK2V617F mutant PVB1.4) derived from the same MPN patient were obtained from Drs. Zhaohui Ye and Linzhao Cheng (Johns Hopkins University)31 . Both JAK2 wild-type (PVB1.11) and JAK2V617F mutant (PVB1.4) iPS cell lines were differentiated into ECs using a modified iPS differentiation protocol adapted from Patsch et al.32 and Guadall et al.33 (see Figure 4A). Day 0: iPS cells were dissociated using Accutase (A6964, Sigma) and seeded on Growth Factor Reduced Basement Membrane Matrix-coated plates (Cat. 356230, Corning) at a density of 30,000 cells/cm2 in mTeSR medium with 10uM RevitaCell. Day 1: the medium was replaced by N2B27 medium, which is consisted of a 1:1 mixture of DMEM:F12 (Cat. 11320082, ThermoFisher) and Neurobasal medium (Cat. 21103049, ThermoFisher) supplemented with N2 (Cat. 17502048, ThermoFisher) and B27 without vitamin A (Cat. 12587010, ThermoFisher), containing 7μM of CHIR99021 (Cat. 4423/10, R&D Systems) and 25ng/mL recombinant human BMP4 (Cat. 314-BP, R&D Systems), at ~0.7ml of medium per cm2 of cultured area. Day 4: the medium was replaced with StemPro-34 SFM (Cat. 10639011, ThermoFisher) containing 200ng/mL Vascular Gndothelial Growth Factor (VEGF)-165 (Cat. 100-20, Peprotech) and 2μM Forskolin (Cat. ab120058, Abcam), at ~0.3ml of medium per cm2 of cultured area. Day 6-7: cells were dissociated using Accutase and separated using human CD144 Microbeads (Cat. 130-097-857, Miltenyi). Isolated CD144+ cells were plated at a density of ~15,000- 25,000 cells/cm2 on human Fibronectin-coated dishes (Cat. 354008, Corning) in StemPro-34 SFM supplemented with 50ng/mL VEGF-165. Day 8-9: the medium was replaced with StemPro-34 SFM supplemented with 50ng/mL VEGF-165 and 8μM SB431542 (Cat. 1614/10, R&D systems). From Day 12 onwards, ECs were cultured in EGM-2 medium (Cat CC-3162, Lonza) supplemented with 8μM SB431542. The medium was replaced every other day. Cells at confluence were dissociated using 0.05% Trypsin-EDTA (Cat. 25300054, ThermoFisher) and cryopreserved in freezing medium consisting 90% FBS and 10% DMSO for future experimental use. The iPSderived wild-type ECs maintained their EC identity up to at least passage 8, although cell growth was significantly slowed after passage 6.

extract_protocol:
Briefly, total RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) from human iPS-derived JAK2 wild-type and JAK2V617F mutant ECs treated with or without AMM2 between passage 3 and passage 5 (~15 days).
The isolated RNA samples were sent to Novogene, Inc. for bulk RNA sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads and used to generate sequencing libraries using NEBNext Ultra™ RNA Library Prep Kit for Illumina® (New England BioLabs, MA, USA). The library preparations were sequenced on an Illumina platform.

treatment_protocol: Human iPS-derived ECs were cultured in EGM-2 medium supplemented with 8μM SB431542 as described above. To inhibit TPO/MPL signaling, cells were treated with 100ng/ml of anti-MPL antibody (AMM2, IBLAmerica).

value: iPSC-derived endothelial cells

value: Wild-type

value: AMM2 MPL inhibitor


title: PF-382_ATACseq_KO_clone28_rep2

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

data_processing:
HiChIP data were mapped to hg19 human genome reference and analyzed using MAPS41 v2.0 as implemented within the Arima Genomics bioinformatics pipeline available at https://github.com/ijuric/MAPS. ChIP-seq and ATAC-seq reads were mapped to GRCh38 human genome reference by BWA. MACS2 (version 2.1.1) was used for peak calls.
Assembly: hg19/hg38
Supplementary files format and content: BigWig and Hic for HiChIP. BigWig for ChIP and ATAC

growth_protocol: Cell lines were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine. PDX cells were not cultured before performing ChIP-seq

extract_protocol:
Freshly cultured cells were counted using trypan blue and a cell suspension volume corresponding to 6 million live cells was washed once with PBS (-Ca2+ -Mg2+) and then crosslinked in a volume of 5 mL PBS with 2% formaldehyde for 10 minutes at room temperature, followed by quenching with Stop Solution 1 according to the Arima protocol for HiChIP, or  Glycine Solution (10X, Cell Signaling, #7005S) according to SimpleChiP kit (Cell Signaling, #56383) for ChIP-seq. For ATAC-seq, 50,000 cells were taken from culture and washed once in cold PBS before proceeding with cell lysis, nuclei extraction, tagmentation and library preparation according to the Omni-ATAC protocol (PMID 28846090)
All H3K27ac HiChIP experiments were performed using the Arima-HiC+ kit (Arima Genomics A101020) according precisely to the manufacturer’s protocols (Arima-HiC+ Document numbers A160168 v00 (HiChIP) and A160169 v00 (library preparation)). All ChIPseq experiments were performed using the SimpleChiP kit (Cell Signaling, #56383) according precisely to the manufacturer’s protocols.

treatment_protocol: no treatment

value: leukemia

value: CRISPR-edited STAG2 KO


title: output1


title: iPSC EC, wild-type, untreated

value: Untreated


title: PF-382_ATACseq_KO_clone28_rep1


title: AT2 cells (4T1 Distal) rep1


title: AT2 cells (4T1 Distal) rep2


title: PF-382_ATACseq_KO_clone23_rep2


title: iPSC EC, JAK2V617F, AMM2 treated


title: Ctrl_rep5

city: Turku

first: Petra

last: Sipilä

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

data_processing:
The base calling was done using Illumina's standard bcl2fastq software
Read alignment was done using STAR (v. 2.5) using the method of Maximal Mappable Prefix (MMP)
Genewise read counts were calculated using HTSeq (v.0.6.1)
Assembly: mm10
Supplementary files format and content: Processed data file is comma delimited text file containing the genewise read counts for each sample.

source_name: 3D organoids

growth_protocol: 3D organoids were cultured in DMEM/F12 supplemented with 15% iFBS, 5% L-glutamine, 2,5% Pen-Strep, 1 ug/ml hydrocortisone, 0.2 U/ml insulin, 0.1 nmol/l cholera toxin and 25 ng/ml EGF

extract_protocol:
The organoids were harvested on day 12 of culture from Matrigel droplets by using ice cold 5mM EDTA-PBS. Replicate droplets were collected, combined and incubated on ice in a large volume of buffer until the Matrigel had dissolved. The solution containing soluble Matrigel and the organoids was centrifuged (100 x g, 5 min, 4C) and the pellet was washed once with ice cold PBS. Total RNA was isolated from cell pellets by using Trisure reagent (Bioline, USA) according to manufacturer’s instruction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: 3D organoids

value: epididymal epithelial mE-Cap18

value: Ctr


title: AT2 cells (CT26 Niche) rep3


title: AT2 cells (CT26 Distal) rep3


title: Runx_rep5

value: douple deletion of Runx1 and Runx2


title: Ctrl_rep4


title: PF-382_ATACseq_WT_clone20_rep2

value: CRISPR-edited control


title: iPSC EC, JAK2V617F, untreated


title: Runx_rep4


title: PF-382_ATACseq_KO_clone23_rep1


title: PF-382_ATACseq_WT_clone20_rep1


title: Ctrl_rep3


title: Runx_rep3


title: MOLT-14_ATACseq_STAG2_rep2

value: transduced with STAG2 vector


title: Ctrl_rep1


title: Ctrl_rep2


title: PF-382_ATACseq_WT_clone19_rep1


title: PF-382_ATACseq_WT_clone19_rep2


title: MOLT-14_ATACseq_STAG2_rep3


title: MOLT-14_ATACseq_EV_rep1

value: transduced with empty vector


title: HSC-D6

first: chen

last: minqi

address: No.74, 2nd Zhongshan Road

institute: Sun Yat-sen University

data_processing:
RNA seq reads were aligned to mouse genome GRCm38 and gene annotation from the Ensembl database. For read alignment and expression quantification, low quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.5.0, Babraham Bioinformatics). The remaining pair-end reads were mapped to the reference genome by Salmon (v0.03.1, COMBINE-lab) with ENCODE options. The uniquely mapped reads were counted and transformed to transcripts per kilobase millionreads (TPM)
Assembly: GRCm38
Supplementary files format and content: ABCD_edgeR_CPM_annotated.csv with raw counts matrices

source_name: HSCs purified from challenged wild-type C57BL/6J mice with Listeria monocytogenes (LM)  at 3 days after the secondary LM challenge。

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8 weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Low input RNA seq was performed according to published scRNA seq protocols with modifications (Picelli et al., 2014). Briefly, FACS-sorted 1500 Lin– Scal1+ c-Kit+ CD48– CD150+ (HSC) (3-5 µL) of each sample were transferred into 40 µL cell lysis buffer prepared by adding 2 µL of RNase inhibitor to 38 µL of a 0.25% (v/v) Triton X-100 solution. Quickly vortex the tube to mix, and then purify RNA using 80 µL VAHTS RNA Clean Beads (N412, Vayzme), following reverse transcription with 5 µL purified RNA and 15 µL RT mix of each sample. cDNA purified with VAHTS DNA Clean Beads (N411, Vazyme) was used to perform PCR enrichment with 13 cycles of amplification. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit (Q3285, Guangzhou IGE biotechnology ltd) after purification. TruePrepTM DNA library Prep Kit V2 (TD503, Vazyme) was used to prepare RNA seq library following the manufacturer’s protocol. Libraries were sequenced as paired 150 bp using NovaSeq-PE150.

value: HSCs

value: bone marrow

value: 6-8 weeks

value: wild type


title: HSC-D4


title: Runx_rep1


title: MOLT-14_ATACseq_EV_rep2


title: HSC-D3


title: HSC-D5


title: SJALL067460_PDX_ChIPseq_CTCF

value: PDX cells

tag: chip antibody

value: CTCF (Active Motif #91285)

value: no treatment


title: HSC-D2


title: PER-117_ChIPseq_CTCF_input

value: leukemia

value: input


title: PER-117_ChIPseq_CTCF


title: HSC-C6

source_name: HSCs purified from challenged wild-type C57BL/6J mice with Listeria monocytogenes (LM) at 6 weeks after LM infection.


title: HSC-D1


title: Runx_rep2


title: MOLT-14_ChIPseq_CTCF_STAG2_rep2_input


title: AT2 cells (4T1 Niche) rep2

value: Alveolar type II cells


title: HSC-C5


title: MOLT-14_ChIPseq_CTCF_STAG2_rep1_input


title: MOLT-14_ATACseq_STAG2_rep1


title: MOLT-14_ChIPseq_CTCF_STAG2_rep2


title: HSC-C3


title: MOLT-14_ChIPseq_CTCF_STAG2_rep1


title: HSC-C4


title: SJALL067460_PDX_ChIPseq_CTCF_input


title: HSC-C2


title: HSC-C1


title: MOLT-14_ChIPseq_CTCF_EV_rep2_input


title: HSC-B6

source_name: HSCs purified from challenged wild-type C57BL/6J mice with Listeria monocytogenes (LM) at 3 days after LM infection.


title: HSC-B5


title: MOLT-14_ChIPseq_CTCF_EV_rep1_input


title: HSC-B4


title: MOLT-14_ChIPseq_CTCF_EV_rep1


title: HSC-B3


title: MOLT-14_ChIPseq_CTCF_EV_rep2


title: Sample 6–DAbseq (DAb-seq: Protein)

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description: see file Sample6_DAbseq.h5 linked to the DNA sample

data_processing:
FASTQ files generated by the sequencer were processed using the Tapestri Pipeline V2, which included adapter trimming and sequence alignment (Burrows-Wheeler Aligner) to the human genome (GRCh37/hg19), barcode correction, and cell find. For variant calling and genotyping, we processed as previously described 1.
Assembly: hg19
Supplementary files format and content: Raw read counts and filtered genotype calls for single-cell DNA seq
Supplementary files format and content: Raw and normalized read counts for single-cell antibody seq
Library strategy: multiomic single-cell DNA and antibody sequencing (Dab-seq)

molecule: protein

source_name: Bone Marrow

extract_protocol:
BM MNCs were isolated from each sample using the standard gradient separation approach with Ficoll-Paque PLUS (GE Healthcare Lifesciences, Marlborough, MA).
According to the manufacturer's protocol, single-cell library DNA preparation was performed using the Tapestri Platform and reagents (MissionBio). Briefly, cryopreserved bone marrow mononuclear cells were thawed, washed with RPMI1640 supplemented with 40% FBS, 1% BSA, and 5 mM EDTA, and counted using a Countess cell counter (Invitrogen). BMNCs were normalized to 25,000 cells/μL in 40 μL and incubated with Human TruStain FcX (BioLegend, catalog# 422301), Blocking buffer in 1× staining buffer for 15 minutes on ice. Next, cells were stained with TotalSeq™-D Human Heme Oncology Cocktail (Biolegend, catalog# 399906), CD99 (Biolegend, catalog# 371325), and CD366 (Biolegend, catalog# 345057) AOCs for 30 minutes on ice. Following staining, cells were washed three times in wash buffer and were loaded onto the Tapestri instrument for single-cell encapsulation, lysis, and barcoding with 2 μmol/L antibody tag forward primer. The DNA from barcoded cells was amplified via multiplex PCR using a targeted myeloid panel that included 279 amplicons across 37 genes associated with myeloid malignancies (https://designer.missionbio.com/catalogpanels/Myeloid-MDACC). DNA libraries were extracted from the droplets, followed by purification with Ampure XP beads (Beckman Coulter). The purified DNA libraries were indexed and then sequenced on Illumina's NovaSeq 6000 SP with 250-bp paired-end multiplexed runs. Protein PCR products, which exist in the supernatant from the Ampure XP bead purification step, were isolated by a 5-minute incubation with 2 μL 5′ biotin oligo for 5 minutes at 96°C, followed by a 5-minute incubation on ice. Isolated proteins were washed using 2× binding and washing buffer and streptavidin beads. Protein libraries were generated using the washed proteins, library template, and i5/i7 indices via PCR. The protein library PCR product was cleaned again using Ampure XP beads. Protein libraries were quantified, quality checked, and sequenced on Illumina's NovaSeq 6000 S4 with 150-bp paired-end multiplexed runs.

value: Bone Marrow

value: BM MNCs

value: TET2 Q557X, TET2 G223Mfs*28, CBL C384Y, CBL F378Ifs*5, SRSF2 P95L, ASXL1 R965X, RUNX1 R201X

value: Azacitidine

tag: library type

value: Antibody


title: HSC-A6

source_name: HSCs from naïve mice.


title: MOLT-14_ChIPseq_CTCF


title: Sample 6–DAbseq (DAb-seq: DNA)

value: scDNA


title: Sample 5–DAbseq (DAb-seq: Protein)

description: see file Sample5_DAbseq.h5 linked to the DNA sample

value: TET2 Q557X, TET2 G223Mfs*28, CBL C384Y, CBL F378Ifs*5, SRSF2 P95L

value: Untreated


title: HSC-B1

value: HSCs

value: bone marrow


title: HSC-A5

value: 6-8 weeks

value: wild type


title: HSC-A4


title: Sample 4–DAbseq (DAb-seq: Protein)

description: see file Sample4_DAbseq.h5 linked to the DNA sample

value: NRAS G12R, KRAS T58K, TET2 N1487Kfs*81, ASXL1 G646Wfs*12, SRSF2 P95R


title: MOLT-14_ATACseq_EV_rep3

value: transduced with empty vector


title: HSC-A3


title: Sample 3–DAbseq (DAb-seq: Protein)

description: see file Sample3_DAbseq.h5 linked to the DNA sample


title: MOLT-14_ChIPseq_CTCF_input

value: leukemia

value: no treatment


title: Sample 3–DAbseq (DAb-seq: DNA)


title: HSC-A2


title: HSC-A1


title: nHSC

data_processing:
ATAC-seq reads were trimmed  had a quality score > 30, using trim_galore, discarding reads left with < 20 bp
ATAC-seq reads were aligned to the UCSC mm10 genome using Bowtie2 .
ATAC-seq reads were shifted by deepTools.
Peaks were called using MACS2  with the significance cut-off q-value <=0.05.
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8 weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Library amplification was generated according to a protocol based on Corces et al Nature Method 2017.


title: Sample 4–DAbseq (DAb-seq: DNA)


title: HSC-B2


title: BBM4

city: Fujisawa-shi

first: Shin-ichiro

last: Takayanagi

state: Kanagawa

address: 2-26-1, Muraoka-Higashi

department: KIRIN Central Research Institute

institute: Kirin Holdings

data_processing:
Sequenced on a NovaSeq6000 using NovaSeq Control Software v1.4.0
Real Time Analysis v3.3.3.
bcl2fastqv2 v2.20
RSEM v1.3.0
STAR v2.6.0a
Assembly: The human genome GRCh37 and corresponding annotation Ensembl were obtained from Illumina's iGenomes project.
Supplementary files format and content: Expected counts
Supplementary files format and content: Transcript per million (TPM)

source_name: Peripheral blood

extract_protocol:
RNeasy Mini kit (QIAGEN, 74104)
Libraries were prepared from total RNA (RIN>9.6, Agilent 2200 TapeStation) using a SMART-seq v4 Ultra Low Input RNA kit (Takara Bio, Z4888N), Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) and Nextera XT Index Kit v2 (Illumina) and quantified using a Fragment Analyzer (Agilent).

value: Peripheral blood

value: Primary T cells

value: Stem cell memory T cells

value: BBM


title: BBM3


title: BBM1


title: BBM2


title: RERE_CT20_4

description:
JTK_RERE.RNAseq_DD.txt
BIOCYCLE_RERE_DD.tsv

data_processing:
Quality control and adapter trimming was performed using Trimmomatic (version 0.36).
Reads were aligned to the mm10 genome (UCSC) using the HISAT2 aligner (version 2.2.1), and subsequently sorted using SAMtools (version 1.3.1). After alignment, read quantification was performed using featureCounts (version 1.6.0) and the resulting count data was then normalized to generate RPKM values using the edgeR ‘rpkm’ function (version 3.18.1).
Genes exhibiting daily rhythms in expression were identified using the Jonckheere-Terpstra-Kendall (JTK_CYCLE) and BIOCYCLE algorithms. RPKM normalised gene expression values (Log2 transformed) were provided as input. A differential rhythmicity analysis was performed between all four samples using the algorithm DryR.
Genome_build: mm10
Supplementary_files_format_and_content: Text files (.txt) contain the output from the JTK_CYCLE and BIOCYCLE algorithm when applied to the diurnal RNA-seq data sets generated for each clock reconstitution condition. Files contain the rhythmic parameters calculated by the algorithm for each gene detected by RNA-seq. The dryR results file contains the raw output from the algorithm DryR when it is run to compare the rhythmicity of all four clock reconstitution conditions characterised.

source_name: Skin epidermis

growth_protocol: Mice were kept in rooms at 22°C degrees with ad libitum access to a standard chow diet. Prior to sacrifice, mice were maintained in constant darkness for between 156 and 176 hours.

extract_protocol:
Mice were sacrificed at the relevant time by C02 asphyxiation, and their backskin was subsequently removed and stored in ice-cold PBS. The hypodermis was then removed from the skin by vigorous scraping using a scalpel. In a petri dish, the skin was floated on 10ml of 1mg/ml dispase (Sigma Aldrich) (in PBS) for 45 minutes at 37°C to enzymatically separate the epidermis. Using a scalpel, the epidermis was separated from the surface of the skin, and then mechanically disaggregated using surgical scissors. The disaggregated epidermis was placed into 10ml of ice cold PBS + 10% chelated FBS to inactivate dispase, and then sequentially filtered through 100µM and 40µM filters, giving a purified extract of epidermal cells. To extract total RNA, one million epidermal cells were lysed in 500µL TRIzol (Invitrogen), vortexed with 100µL chloroform, and then the resulting aqueous layer containing RNA was isolated. The aqueous layer was mixed with 825µL RLT buffer (Qiagen) and 625µL 100% ethanol to induce RNA precipitation. The sample was further processed using an RNeasy mini kit (Qiagen) in accordance with the manufacturers protocol, and RNA was eluted in molecular biology grade water.
Prior to library preparation, RNA integrity was estimated using an RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent). Libraries were prepared with KAPA Stranded mRNA-Seq IllUMI.fastq.gzna® Platforms Kit (Roche) following the manufacturer´s recommendations. Briefly, 500 ng of total RNA was used for the poly-A fraction enrichment with oligo-dT magnetic beads, following the mRNA fragmentation. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt-ended double stranded cDNA was 3´adenylated and IllUMI.fastq.gzna platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (IllUMI.fastq.gzna) with a read length of 1x51bp+17bp+8bp using, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).

treatment_protocol: To profile circadian transcriptional rhythms, for each genotype, the skin of four eight-week-old mice (all females) was collected at six time points throughout the day. Each time point was separated by four hours, with the first sample collected at lights on (CT0/8:00am).

tag: replicate

tag: gender

value: Female

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre tg/wt

tag: clock reconsitution status

value: Brain and epidermis reconstituted (RERE)


title: RERE_CT20_2

tag: genotype


title: Control4

tag: cell line

tag: cell type

tag: treatment

value: Water


title: RERE_CT20_3

tag: strain


title: RERE_CT16_4


title: Sample 5–DAbseq (DAb-seq: DNA)

tag: tissue

value: Bone Marrow

value: BM MNCs

value: TET2 Q557X, TET2 G223Mfs*28, CBL C384Y, CBL F378Ifs*5, SRSF2 P95L

value: Untreated

value: scDNA


title: RERE_CT20_1


title: Control2


title: RERE_CT16_2


title: mHSC

value: HSCs

value: bone marrow

value: wild type


title: C2_Not_transfected_rep2(C5)

city: Barakaldo

first: Koen

last: Vandenbroeck

state: Bizkaia

address: Plaza Cruces, s/n

institute: Basque Country University / IIS Biobizkaia

data_processing:
fastq files were aligned to human reference genome GRCh38 using Tophat 2.1.0 tool package.
Low quality reads were removed using the packages Samtools 1.2 and Picard tools 2.9.0
Transcripts assembly and gene identification using Bayesian inference methods with Cufflinks v2.2.2
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by by DESeq2
Assembly: human reference genome GRCh38
Supplementary files format and content: Excel file include normalized read counts each sample.

source_name: IMHu-M cell line

growth_protocol: Immortalized human microglia-SV40 (IMhu-M) cellswere grown in high glucose Dulbecco’s Modified Eagle’s medium (DMEM) in 0.1% collagen I pre-coated flasks and placed in a 5% CO2 37 °C.

extract_protocol:
RNA samples were isolated using the NucleoSpin RNA extraction kit (Macherey-Nagel) and processed as per manufacturer’s instructions.
Libraries were prepared using the NEBNext Single Cell/Low input library preparation kit for Illumina, according to the manufacturer’s instructions.

treatment_protocol: IMhu-M cells were either left unstransfected, or transfected with ANKRD55 mRNA using Viromer® mRNA reagent following manufacturer’s recommendations and incubated for 24 hours.

value: IMHu-M cell line

value: microglia


title: T2_ANKRD55_rep2(E5)


title: RERE_CT12_4


title: RERE_CT12_2


title: RERE_CT16_1


title: T1_ANKRD55_rep1(D5)


title: TELOEC_ATAC_SYN+JQ1_REP2

city: Nashville

first: Lindsey

middle: "Joey"

last: Stolze

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

data_processing:
Reads were mapped to hg38 using bowtie2
ATAC: Used the encode pipeline to map and call peaks (macs2)
CUTandRUN: HOMER was used to call peaks (findPeaks) that were then merged per protein
HOMER getDifferentialPeaks workflow was used to call differential peaks
Assembly: hg38
Supplementary files format and content: peakfiles for each genotype-protein pull down

source_name: teloHAEC

growth_protocol: TeloHAEC (ATCC: CRL-4052) cells were subcultured using Vascular Cell Basal Medium (ATCC: PCS-100-030) supplemented with Endothelial Cell Growth Kit-VEGF (ATCC: PCS-100-041) at 37C and 5% CO2. Cells were cultured until p10 and media was changed every 3 days. Cells were changed into media lacking hydrocortisone 16-20 hours before stimulation.

extract_protocol:
ATAC-seq:Followed protocol from Grandi et al 2022, Nature Protocols, https://doi.org/10.1038/s41596-022-00692-9 CUT&RUN: CUT&RUN was performed as previously described with a few modifications. 1xe6 cells were fixed in 0.1% Formaldyhde for 1 minute before fixation was quenched with 1.5M glycine for 1 minute. Cells were bound to 10uL of activated My-One Concavalin beads per IP. Cells and beads were washed with buffers containing (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA Protease and Phosphatase Inhibitors (Thermo Scientific, 78440). Cells were permeabilized in the buffer above plus 0.01% digitonin and 0.7ug of each respective antibody was added to the buffer above plus 0.01% digitonin and 250mM EDTA. Samples then incubated overnight on a nutator at 4C. Samples were washed in the buffer above plus 0.01% digitonin and then pAG-MNase was added to the samples and bound for 1 hour at 4C, after which 100mM CaCL2 was added and pAG-MNase cleavage went for 30 minutes with samples submerged in ice. DNA was purified via a phenol-chloroform isolation after which the purified DNA was utilized to generate sequencing libraries.
ATAC-seq:Followed protocol from Grandi et al 2022, Nature Protocols, https://doi.org/10.1038/s41596-022-00692-9 CUT&RUN:DNA libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB #E7645) with the following PCR cycling adjustments for the PCR Enrichment of adaptor ligated DNA  a. 45 sec at 98ºC  b. 15 sec at 98ºC  c. 10 sec at 60ºC  d. Repeat Steps b-c for a total of 14 cycles e. 1 min at 72ºC  final extension.

treatment_protocol: TeloHAECs were unstimulated or treated with 50ng/mL IFNg + 25ng/mL TNFa in the presence or absence of DMSO, 2000nM A-485 or 500nM JQ1 for one hour before cells were harvested for ATAC-seq

value: teloHAEC

value: Human Aortic Endothelial Cells

value: Normal

value: 50ng/mL IFNg, 25ng/mL TNFa, and 500nM JQ1


title: RERE_CT8_4

value: Female

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre tg/wt


title: RERE_CT12_3

value: Brain and epidermis reconstituted (RERE)


title: Control3

value: Peripheral blood

value: Primary T cells

value: Stem cell memory T cells

value: Water


title: RERE_CT8_3


title: RERE_CT16_3


title: TELOEC_ATAC_SYN+JQ1_REP1


title: RERE_CT8_1


title: TELOEC_ATAC_SYN+DMSO_REP1

value: 50ng/mL IFNg, 25ng/mL TNFa, and DMSO


title: r2_3D_iWAT_EGM-PGM_woISO [D118]

value: inguinal white adipose tissue

value: Stromal vascular fraction

value: WT

value: Angiogenic and adipogenic differentiation


title: TELOEC_ATAC_SYN+A485_REP2

value: 50ng/mL IFNg, 25ng/mL TNFa, and 2000nM A485


title: TELOEC_ATAC_SYN+DMSO_REP2

value: teloHAEC


title: r1_2D_iWAT_PGM_wISO [D115]

value: Adipogenic differentiation, Isoproteronol treatment

value: Isoproterenol (Sigma, I5627) for 6 hours (final conc. 1 µM)


title: RERE_CT4_2


title: RERE_CT12_1


title: Control1


title: C1_Not_transfected_rep1(B5)

value: IMHu-M cell line

value: microglia


title: RERE_CT8_2

value: Female

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre tg/wt


title: RERE_CT4_3

value: Brain and epidermis reconstituted (RERE)


title: TELOEC_ATAC_NOTX_REP1

value: Human Aortic Endothelial Cells

value: Normal

value: No Treatment


title: TELOEC_ATAC_NOTX_REP2


title: FLAG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_SYN_rep2

data_processing:
Reads were mapped to hg38 using bowtie2
ATAC: Used the encode pipeline to map and call peaks (macs2)
CUTandRUN: HOMER was used to call peaks (findPeaks) that were then merged per protein
HOMER getDifferentialPeaks workflow was used to call differential peaks
Assembly: hg38
Supplementary files format and content: peakfiles for each genotype-protein pull down
Library strategy: CUT&RUN

value: double KO p65 and STAT1, reconstituted FLAG-STAT1 via virus

value: 50ng/mL IFNg and 25ng/mL TNFa

value: M2 FLAG (Mouse Monoclonal Cat:F3165-1MG Lot:SLCJ3741)


title: RERE_CT4_1


title: IgG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_SYN_rep2

value: IgG (Mouse IgG Polyclonal Diaganode Cat:C1540001 Lot:MIG003M)


title: RERE_CT0_3


title: FLAG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_NOTX_rep2


title: IgG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_NOTX_rep2


title: FLAG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_SYN_rep1


title: RERE_CT0_4


title: WT_CT20_4

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv

value: Arntl wt/wt ; K14Cre wt/tg ; Syt10-Cre tg/wt

value: Wild-type (WT)


title: RERE_CT4_4


title: TELOEC_ATAC_SYN+A485_REP1

value: teloHAEC

value: 50ng/mL IFNg, 25ng/mL TNFa, and 2000nM A485


title: RERE_CT0_1


title: IgG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_SYN_rep1


title: RERE_CT0_2


title: FLAG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_NOTX_rep1


title: WT_CT20_2

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagSTAT1_dko-p65-STAT1_CUTandRUN_NOTX_rep1


title: FLAG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_SYN_rep2

value: double KO p65 and STAT1, reconstituted FLAG-p65 via virus


title: WT_CT20_3

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_SYN_rep2


title: WT_CT16_4

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: FLAG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_NOTX_rep2


title: WT_CT20_1

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: WT_CT16_3

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: FLAG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_SYN_rep1


title: WT_CT16_2

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: FLAG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_NOTX_rep1


title: WT_CT12_4

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: WT_CT16_1

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_NOTX_rep1


title: WT_CT12_3

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+JQ1_rep2

value: single KO STAT1, reconstituted FLAG-STAT1 via virus

value: 50ng/mL IFNg, 25ng/mL TNFa, and 500nM JQ1


title: WT_CT12_2

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv

value: Female


title: WT_CT12_1

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: WT_CT8_4

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: WT_CT8_3

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+A485_rep2


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+DMSO_rep2

value: 50ng/mL IFNg, 25ng/mL TNFa, and DMSO


title: WT_CT8_2

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+A485_rep2


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+DMSO_rep2


title: WT_CT4_4

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_NOTX_rep2


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+JQ1_rep2

value: single KO p65, reconstituted FLAG-p65 via virus


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_NOTX_rep2

value: Human Aortic Endothelial Cells


title: WT_CT4_3

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+A485_rep2


title: IgG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_SYN_rep1


title: WT_CT4_1

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: WT_CT0_3

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+JQ1_rep2


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+A485_rep2


title: WT_CT4_2

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: WT_CT0_1

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: WT_CT0_2

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+DMSO_rep2


title: BRE_CT20_4

description:
JTK_BrainRE.RNAseq_DD.txt
BIOCYCLE_BrainRE_DD.tsv

value: Arntl stopFL/stopFL ; K14Cre wt/wt ; Syt10-Cre tg/wt

value: Brain Reconsituted (BRE)


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+JQ1_rep2


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+DMSO_rep2


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_NOTX_rep2

value: No Treatment


title: WT_CT8_1

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_NOTX_rep2


title: BRE_CT20_2


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+JQ1_rep1


title: IgG_TELOEC_flagp65_dko-p65-STAT1_CUTandRUN_NOTX_rep2


title: BRE_CT16_4


title: BRE_CT20_1


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+A485_rep1


title: BRE_CT16_3


title: WT_CT0_4

description:
JTK_WT.RNAseq_DD.txt
BIOCYCLE_WT_DD.tsv


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+A485_rep1


title: BRE_CT16_2


title: BRE_CT16_1


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+DMSO_rep1


title: BRE_CT12_3


title: FLAG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_NOTX_rep1


title: BRE_CT12_2


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+DMSO_rep1


title: BRE_CT12_1


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+JQ1_rep1


title: BRE_CT12_4


title: BRE_CT20_3


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_NOTX_rep1


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+JQ1_rep1


title: BRE_CT8_4


title: BRE_CT8_3


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+A485_rep1


title: BRE_CT8_2


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+A485_rep1


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+DMSO_rep1


title: BRE_CT8_1


title: BRE_CT4_4


title: IgG_TELOEC_flagSTAT1_sko-STAT1_CUTandRUN_SYN+JQ1_rep1


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_SYN+DMSO_rep1


title: BRE_CT4_3


title: FLAG_TELOEC_flagp65_sko-p65_CUTandRUN_NOTX_rep1


title: IgG_TELOEC_flagp65_sko-p65_CUTandRUN_NOTX_rep1


title: BRE_CT4_2


title: Acute cellular rejection B

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

description: Spatial transcriptome sequencing of fresh frozen tissue, without OCT.

data_processing:
*library strategy: Spatial Transcriptomics
Sequences were aligned to the hg38 human reference genome, the counts separated by cell, the data filtered and processed using Space Ranger version 1.3.1 according to manufacturer specifications
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene Ids
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: Human Kidney

extract_protocol:
Fresh frozen tissue, without OCT. 10 µm sections were cut with cryostat.
Spatial Transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides and Reagents, according to “Visium Spatial Gene Expression Reagent Kits”(CG000239 Rev E) user guide

value: Human Kidney

value: Acute cellular rejection


title: BRE_CT0_4


title: BRE_CT4_1


title: Articular cartilage-derived cells, 0kPa, rep3

city: Suita

first: Shohei

last: Oyama

state: Osaka

address: 2-2 Yamada-oka

department: Department of Musculoskeletal Regenerative Medicine

institute: Osaka University Graduate School of Medicine

description: AC 0kPa_3

data_processing:
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) and read count was calculated using Cufflinks version 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text-file includes read counts for each sample

source_name: Articular cartilage-derived cells

growth_protocol: The cultured cells (5 × 105 cells/scaffold) were suspended in DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin,  then gently mixed with an equal volume of 1% atelocollagen gel (Koken Co. Ltd., Tokyo, Japan) on ice to produce a cell suspension in 0.5% collagen solution. The cell suspension was incorporated into collagen scaffolds (Atelocollagen Sponge Mighty, Koken; 5 and 3 mm in diameter and thickness, respectively) by centrifugation at 500 × g for 5 minutes.  The cell-scaffold constructs were then incubated at 37°C for gelation to produce 3D cell-scaffold constructs. The constructs were cultured on 96-well plates in 200 μL of DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin under free-swelling conditions at 37°C and in 5% CO2.

extract_protocol:
The frozen cell-scaffold were crushed and homogenized using stainless beads shocker. Total RNA extraction and reverse transcription were performed using Trizol (Themo Fisher Scientific), PureLink RNA Purification kit (Thermo Fisher Scientific)
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Using metal pistons, 40-kPa CCL was applied to the cell-scaffold constructs at 0.5 Hz for 1 h per day, followed by free-swelling for 23 h. This procedure was repeated seven times over a period of seven days.

value: Articular cartilage-derived cells


title: BRE_CT0_3


title: Meniscus-derived cells, 40kPa, rep3

description: MC 40kPa_3

source_name: Meniscus-derived cells

value: Meniscus-derived cells


title: Articular cartilage-derived cells, 40kPa, rep3

description: AC 40kPa_3


title: Meniscus-derived cells, 0kPa, rep3

description: MC 0kPa_3


title: EpiRE_CT20_4

description:
JTK_EpiRE.RNAseq_DD.txt
BIOCYCLE_EpiRE_DD.tsv

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre wt/wt

value: Epidermis Reconsituted (EpiRE)


title: EpiRE_CT20_3


title: EpiRE_CT20_1


title: Articular cartilage-derived cells, 0kPa, rep2

description: AC 0kPa_2


title: Synovium-derived cells, 0kPa, rep3

description: SY 0kPa_3

source_name: Synovium-derived cells

value: Synovium-derived cells


title: Synovium-derived cells, 40kPa, rep3

description: SY 40kPa_3


title: BRE_CT0_1


title: EpiRE_CT20_2


title: Articular cartilage-derived cells, 40kPa, rep2

description: AC 40kPa_2


title: Meniscus-derived cells, 40kPa, rep2

description: MC 40kPa_2


title: Meniscus-derived cells, 0kPa, rep2

description: MC 0kPa_2


title: EpiRE_CT16_3


title: Synovium-derived cells, 0kPa, rep2

description: SY 0kPa_2


title: Articular cartilage-derived cells, 40kPa, rep1

description: AC 40kPa_1


title: EpiRE_CT16_2


title: EpiRE_CT12_4


title: Meniscus-derived cells, 40kPa, rep1

description: MC 40kPa_1


title: Articular cartilage-derived cells, 0kPa, rep1

description: AC 0kPa_1


title: EpiRE_CT12_3


title: EpiRE_CT12_2


title: Meniscus-derived cells, 0kPa, rep1

description: MC 0kPa_1


title: Synovium-derived cells, 0kPa, rep1

description: SY 0kPa_1


title: EpiRE_CT8_4


title: EpiRE_CT12_1


title: EpiRE_CT16_1


title: EpiRE_CT8_3


title: Synovium-derived cells, 40kPa, rep1

description: SY 40kPa_1


title: EpiRE_CT16_4


title: Interstitial fibrosis and tubular atrophy (IFTA) [C]

data_processing:
*library strategy: Spatial Transcriptomics
Sequences were aligned to the hg38 human reference genome, the counts separated by cell, the data filtered and processed using Space Ranger version 1.3.1 according to manufacturer specifications
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene Ids
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format

tag: diagnostic category

value: IFTA


title: EpiRE_CT8_1


title: EpiRE_CT8_2


title: Synovium-derived cells, 40kPa, rep2

description: SY 40kPa_2


title: EpiRE_CT4_4


title: Acute cellular rejection [A]


title: OvCAR3Sph2

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description: spheroid

data_processing:
RNA-Seq reads were mapped to the human genome (hg38, Genome Reference Consortium)  using STAR (v2.7.0f)
Counting of the reads was performed with RSEM (v1.3.1) using the ensembl annotation GRCh38.101
Assembly: hg38
Supplementary files format and content: tab-delimited text file of rsem expected counts

source_name: cell line

growth_protocol: Cells were cultured in 96-well flat-bottom (for monolayer) and ultra-low attachment U-bottom (for spheroids) plates for 3 days. Cells were cultured in phenol red-free RMPI 1640 medium supplemnented with 20% foetal bovine serum and 1% penicillin-streptomycin

extract_protocol:
RNA was prepared from cell cultures using the RNeasy microkit.
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc).

value: cell line

value: malignant cells


title: OvCAR3Sph1

description: spheroid


title: EpiRE_CT4_3

value: Female


title: G164Sph2

description: spheroid


title: EpiRE_CT4_1


title: OvCAR3Mono2

description: monolayer


title: EpiRE_CT4_2


title: EpiRE_CT0_4


title: EpiRE_CT0_3


title: EpiRE_CT0_2


title: G164Sph1

description: spheroid


title: G164Mono2

description: monolayer


title: EpiRE_CT0_1


title: G164Mono1

description: monolayer


title: RERE_ZT20_4

description:
JTK_RERE.RNAseq_LD.txt
BIOCYCLE_RERE_LD.tsv

extract_protocol:
Mice were sacrificed at the relevant time by C02 asphyxiation, and their backskin was subsequently removed and stored in ice-cold PBS. The hypodermis was then removed from the skin by vigorous scraping using a scalpel. In a petri dish, the skin was floated on 10ml of 1mg/ml dispase (Sigma Aldrich) (in PBS) for 45 minutes at 37°C to enzymatically separate the epidermis. Using a scalpel, the epidermis was separated from the surface of the skin, and then mechanically disaggregated using surgical scissors. The disaggregated epidermis was placed into 10ml of ice cold PBS + 10% chelated FBS to inactivate dispase, and then sequentially filtered through 100µM and 40µM filters, giving a purified extract of epidermal cells. To extract total RNA, one million epidermal cells were lysed in 500µL TRIzol (Invitrogen), vortexed with 100µL chloroform, and then the resulting aqueous layer containing RNA was isolated. The aqueous layer was mixed with 825µL RLT buffer (Qiagen) and 625µL 100% ethanol to induce RNA precipitation. The sample was further processed using an RNeasy mini kit (Qiagen) in accordance with the manufacturers protocol, and RNA was eluted in molecular biology grade water.
Prior to library preparation, RNA integrity was estimated using an RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent). Libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) following the manufacturer´s recommendations. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 1x51bp+17bp+8bp using, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).

value: Male

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre tg/wt

value: Brain and epidermis reconstituted (RERE)


title: RERE_ZT20_2


title: RERE_ZT20_3


title: BRE_CT0_2

value: Arntl stopFL/stopFL ; K14Cre wt/wt ; Syt10-Cre tg/wt


title: TELOEC_ATAC_TNFA_RB9742_REP2

data_processing:
RNA-seq
Reads were mapped to hg38 using TopHat v2.1.1.
Deseq2 was used to call differential peaks
Novel statistical analysis was performed to identify synergystically induced genes
Assembly: hg38
Supplementary files format and content: count
ATAC-Seq
Reads were mapped to hg38 using bowtie2
HOMER workflow was used to call differential peaks
Assembly: hg38
Supplementary files format and content: .narrowPeak.gz

extract_protocol:
Followed protocol from Grandi et al 2022, Nature Protocols, https://doi.org/10.1038/s41596-022-00692-9
Followed protocol from Grandi et al 2022, Nature Protocols, https://doi.org/10.1038/s41596-022-00692-9
ATAC-seq library prep

treatment_protocol: TeloHAECs were treated with 50ng/mL of IFNg, 25ng/mL of TNFa or 50ng/mL IFNg + 25ng/mL TNFa for one hour before cells were harvested for ATAC-seq

value: TeloHAEC

value: Human Aoritc Endothelial Cells

value: Normal

value: 25ng/mL TNFa


title: TELOEC_ATAC_IFNG_RB9742_REP2

value: 50ng/mL IFNg


title: RERE_ZT16_4


title: TELOEC_ATAC_NOTX_RB9742_REP2

value: No Treatment


title: RERE_ZT20_1


title: TELOEC_ATAC_SYN_RB9742_REP1

value: 50ng/mL IFNg + 25ng/mL TNFa


title: RERE_ZT16_3


title: TELOEC_ATAC_IFNG_RB9742_REP1


title: TELOEC_ATAC_TNFA_RB9742_REP1


title: OvCAR3Mono1

description: monolayer


title: RERE_ZT16_1


title: RERE_ZT16_2


title: TELOEC_ATAC_NOTX_RB9742_REP1


title: IFN50ng/mL+TNF-a25ng/mLRep4

extract_protocol:
Harvested with Purelink RNA Mini Kit Lysis buffer with 10 % Betamercaptoethanol
using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490)
NEBNext libraries for RNA-seq

treatment_protocol: TeloHAECs were treated with 50ng/mL of IFNg, 25ng/mL of TNFa or 50ng/mL IFNg + 25ng/mL TNFa for one hour before cells were harvested for RNA


title: RERE_ZT12_3


title: IFN50ng/mL+TNF-a25ng/mLRep2


title: IFN50ng/mL+TNF-a25ng/mLRep1


title: TELOEC_ATAC_SYN_RB9742_REP2


title: TNF-a25ng/mLRep4


title: RERE_ZT12_2


title: IFN50ng/mL+TNF-a25ng/mLRep3


title: RERE_ZT8_4


title: RERE_ZT8_3


title: RERE_ZT8_1


title: TNF-a25ng/mLRep2


title: TNF-a25ng/mLRep1


title: IFN-g50ng/mLRep4


title: RERE_ZT4_4


title: RERE_ZT8_2


title: IFN-g50ng/mLRep3


title: RERE_ZT12_4


title: RERE_ZT4_1


title: IFN-g50ng/mLRep1


title: RERE_ZT0_4


title: NoTreatmentRep4


title: RERE_ZT0_3


title: NoTreatmentRep3


title: RERE_ZT12_1


title: RERE_ZT0_1


title: NoTreatmentRep1


title: TNF-a25ng/mLRep3


title: NoTreatmentRep2


title: WT_ZT20_4

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv

value: Arntl wt/wt ; K14Cre wt/tg ; Syt10-Cre tg/wt

value: Wild-type (WT)


title: WT_ZT20_3

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PAX-N6-2_48h

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

institute: Yangzhou University

data_processing:
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 4200 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration.
Tophat v2.1.0 were used to map the cleaned reads to the human h38 reference genome with two mismatches. After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Significant differentially expressed (SDE) genes were identified using Cuffdiff.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR)
Assembly: human h38 reference genome
Supplementary files format and content: tab-delimited text files include coutn and FPKM values for each sample.

source_name: 293T cells

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, USA) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To evaluate the role of specific amino acids of PA-X in inhibiting host  protein expression, 293T cells (24-well plate, 2×105.0 cells/well, in triplicate) were transfected  with 50 ng/well of pCDNA-3.1 encoding PA-X proteins from the parental GD15 virus (PAX) or the mutant PA-X protein or the PCAGGS empty vector as an internal control. and then stored at -80 ℃ for further RNA-seq.

value: 293T cells

value: human embryonic kidney

tag: time


title: PAX-N6-3_48h


title: WT_ZT20_2

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: RERE_ZT4_3


title: PAX-N6-1_48h


title: RERE_ZT4_2


title: PAX-N6-3_24h


title: WT_ZT20_1

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: IFN-g50ng/mLRep2


title: WT_ZT16_4

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: WT_ZT16_3

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: WT_ZT16_2

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PAX-N6-2_24h


title: PAX-N3-3_48h


title: PAX-N6-1_24h


title: PAX-N3-2_48h


title: WT_ZT16_1

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: RERE_ZT0_2


title: WT_ZT12_4

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: WT_ZT12_3

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PAX-N3-2_24h


title: PAX-N3-1_48h


title: WT_ZT12_2

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PAX-N3-1_24h


title: WT_ZT12_1

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: WT_ZT8_3

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: WT_ZT8_4

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PAX-2_48h

value: parental PAX


title: TNPR2

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter
Mapping of the reads were obtained using the STAR program  (Dobin et al., 2013) (v2.6.1a_08-27) against human genome (GRCh38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE.v26 database .
Assembly: GRCh38.94

source_name: HK2 cells treated with propionate(15mM) 24h after stimulation with TNF-α 5ng/ml 3h

growth_protocol: human epithelial renal cell line (HK2) (CRL-2190; ATCC) were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/ streptomycin, 1% insulin transferrin selenite  and 5ng/ml hydrocortisone.

extract_protocol:
PureLink TM RNA Mini kit (Invitrogen), with Dnase treatment. Total RNA was eluted in RNase-free water
Sequencing libraries were prepared following the protocol "TruSeq Stranded mRNA Sample Preparation Guide(Part#15031047Rev.E)" with the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA Single Indexes (Illumina Inc. Cat. # 20020492 and 20020493)

treatment_protocol: Cell were stimulated with thapsigargin (4 μM) in absence or presence  of JQ1 (500nM) for 24h


title: TNPR1


title: WT_ZT8_2

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: WT_ZT8_1

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PAX-1_48h


title: TNF2

source_name: HK2 cells treated with TNF-α 5ng/ml 3h


title: PAX-3_24h


title: TNBU1

source_name: HK2 cells treated with butyrate (3mM) 24h after stimulation with TNF-α 5ng/ml 3h


title: WT_ZT4_4

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PRTN2

source_name: HK2 cells treated with propionate(15mM) 24h before stimulation with TNF-α 5ng/ml 3h


title: TNF1


title: PAX-2_24h


title: WT_ZT4_2

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PAX-N3-3_24h


title: PAX-1_24h


title: BUTN1

source_name: HK2 cells treated with butyrate (3mM) 24h before stimulation with TNF-α 5ng/ml 3h


title: CONTROL2

source_name: HK2 cells


title: TNBU2


title: WT_ZT4_3

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: CONTROL1


title: PAX-3_48h


title: WT_ZT4_1

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv


title: PRTN1


title: PCAGGS-3_24h

value: vector only control


title: PCAGGS-2_24h


title: PCAGGS-1_24h


title: WT_ZT0_3

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv

value: Male


title: torinPoly3

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

data_processing:
Read alignment using HISAT default settings
Alignment to reference genome using rpkmForGenes.py (version 11 April 2013)
Genes mapping to multiple places in genome removed
Gene annotation using RefSeq database
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is a .txt file containing rpkms and raw read counts for each sample obtained by the rpkmForGenes.py script

source_name: ATCC MCF7 cells

growth_protocol: MCF7 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1% L-glutamine (all from Wisent Bio Products).

extract_protocol:
Polysome-profiling
RNAseq libraries were obtained according to the strand specific TruSeq protocol including ribosomal RNA depletion (Ribo Zero)

treatment_protocol: MCF7 cells were serum starved for 12h prior treatment and treated with 4.2nM DMSO or 4.2nM insulin or 4.2nM insulin + 250nM torin1

value: breast adenocarcinoma

tag: morphology

value: Epithelial-like

tag: rna

value: Polysome-associated

value: Insulin + torin1


title: torinPoly1


title: torinPoly2


title: torinCyto4

value: cytosolic

value: Insulin + torin4


title: 72_GEO-PI-72

city: Saint Genes Champanelle

first: Daniel

last: Bechet

address: Theix

department: UNH

country: France

institute: INRA

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing and trimming were performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the human genome (UCSC GRCh38/hg38) with a set of gene model annotations (genes.gtf downloaded from UCSC on October 27 2019 ; GeneIDs come from the NCBI: gene2refseq.gz).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene (Symbol|NCBI GeneID) and every sample

source_name: vastus lateralis muscle

extract_protocol:
Total RNA was isolated using a TissueRuptor and RNeasy Fibrous Tissue Mini Kit (QIAGEN) with an on-column DNase digestion (RNase-Free DNase Set, QIAGEN) to avoid genomic DNA contamination. Integrity of RNA samples was verified using an Agilent Bioanalyser with the RNA 6000 Nano labchip® kit (Agilent). Concentration and purity were determined with a Nanodrop ND-1000 spectrophotometer.
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions and sequenced on two lanes on an Illumina NovaSeq 6000 (single-end, 100bp, flow cell S2).

tag: group

tag: Sex

value: male

tag: age (years)

tag: appendicular lean mass (alm)

value: stable high

tag: alm variation (%/year)


title: WT_ZT0_2

first: Thomas

last: Mortimer

address: Carrer Baldiri Reixac 10-12

institute: IRB Barcelona

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv

source_name: Skin epidermis

tag: replicate

tag: time point

tag: gender


title: torinCyto2


title: torinCyto3


title: WT_ZT0_1

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv

tag: genotype

tag: clock reconsitution status


title: torinCyto1

tag: treatment


title: 70_REY-PI-70

value: sarcopenic


title: insulinPoly4

value: insulin


title: BRE_ZT20_4

description:
JTK_BrainRE.RNAseq_LD.txt
BIOCYCLE_BrainRE_LD.tsv

tag: strain

value: Arntl stopFL/stopFL ; K14Cre wt/wt ; Syt10-Cre tg/wt

value: Brain Reconsituted (BRE)


title: 69_DOL-RA-68

value: stable low


title: insulinPoly3

tag: tissue


title: insulinPoly2


title: BRE_ZT20_3


title: insulinPoly1


title: torinPoly4


title: 68_PUP-YV-69

value: female


title: insulinCyto4


title: BRE_ZT20_2


title: WT_ZT0_4

description:
JTK_WT.RNAseq_LD.txt
BIOCYCLE_WT_LD.tsv

value: Arntl wt/wt ; K14Cre wt/tg ; Syt10-Cre tg/wt

value: Wild-type (WT)


title: 67_DRE-PI-67


title: insulinCyto2


title: insulinCyto1


title: BUTN2

tag: cell line


title: ctrlPoly4

value: DMSO


title: 66_BAL-PA-66


title: ctrlPol3

value: breast adenocarcinoma


title: 71_BOU-NI-71


title: ctrlPoly2

value: Epithelial-like


title: 65_BON-MI-65


title: BRE_ZT16_3

value: Male


title: 64_FON-AN-64


title: ctrlCyto3


title: 63_TIB-RO-63


title: insulinCyto3


title: ctrlCyto1


title: ctrlCyto2


title: 62_MON-AR-62


title: e15wt_idna_yz057

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

description: e15wt_gli3.idr.optml.narrow.peaks.mm10.bed.trk.gz

data_processing:
Paired end reads were trimmed to 85x85bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements.
Paired end reads that mapped to repeat elements were discarded. The remaining reads were mapped using Bowtie2 to the mm10 genome.
Duplicate mapped reads were removed using samtools.
The repeat-filtered, duplicate-removed control (input DNA) replicate mappings were concatenated into a single set for use in IDR processing.
The repeat-filtered, duplicate-removed mappings were divided into 2 pseudo replicates for each sample for use in IDR processing.
Peaks were called for the replicates and pseudo replicates using MACS2 with a very permissive p-value cutoff of 0.5 to generate a large set of peaks for processing by IDR.
The top 100,000 MACS2 peaks for the replicates and pseudo replicates were processed by IDR and then filtered using  thresholds for the  original replicates, self pseudo replicates, and pooled pseudo replicates of 0.01, 0.02, 0.01 respectively
The optimal set of peaks selected by IDR using the above criteria were extracted into a narrowPeak bed file.
Assembly: mm10
Supplementary files format and content: narrowPeak bed file

source_name: cerebral cortex

extract_protocol:
E15 wild type cortices were dissected, fixed for 10 min with 1% formaldehyde and neutralized with glycine. The cells were lysed, and the chromatin was sheared into 100∼300 bp fragments. Immunoprecipitation reactions were performed using the Gli3 antibody
For ChIP-seq, sequencing libraries were generated from the ChIP-ed DNA and input DNA for control using Ovation Ultralow System V2 kit according to the manufacturer’s protocol.

value: cerebral cortex

tag: developmental stage

tag: antibody

value: input DNA

value: wt

value: ChIPseq


title: e15wt_idna_yz053


title: BRE_ZT16_2

city: Barcelona


title: BRE_ZT20_1


title: e15wt_idna_yz049


title: BRE_ZT12_3


title: 61_DUH-JE-61

value: male

value: stable high


title: e15wt_gli3_yz056


title: BRE_ZT16_1


title: BRE_ZT12_4


title: 60_FON-GE-60

value: gain


title: BRE_ZT16_4

value: Arntl stopFL/stopFL ; K14Cre wt/wt ; Syt10-Cre tg/wt


title: BRE_ZT12_1

value: Brain Reconsituted (BRE)


title: e15wt_gli3_yz048


title: ctrlPoly1

tag: morphology

tag: rna

value: Polysome-associated


title: BRE_ZT12_2


title: 59_AUV-AN-59

tag: group

tag: Sex